The Quest for John Watson
by TheVeiledArch
Summary: When John mysteriously disappears and the master of deduction can't figure out why, it's time for a certain Time Lord to step in and help.
1. The Reunion

Chapter 1 - The Reunion

"Oh, Sherlock, how you've _grown!_" the Doctor exclaimed. Sherlock groaned.

"I'm an adult now, thank you," he said exasperatedly.

"Come on, you used to think that was funny."

"Not anymore. I've grown up."

"Pity." the Doctor said. He turned around quickly, evidently having lost interest in the conversation. He pranced about the flat, picking books up and flipping through them, sitting in chairs and examining the cups and plates strewn about. He finally settled in the chair to the left of the fireplace. He crossed his legs, folded his hands, and looked up happily at Sherlock. "Quite a nice place you've got here. Bit messy, but then, I like it. Don't redecorate." Sherlock turned away from the Doctor. He crossed the room and flopped onto the couch.

"That's John's chair," was all he said. Then he put his head in his hands and sighed. The Doctor looked at him worriedly and jumped out of the chair.

"I can stand! Perfectly fine with standing." The Doctor stood quite awkwardly, rocking back and forth on his feet, hands behind his back. He cleared his throat.

"Oh, sit in the damn chair. That's not the point," Sherlock said. He fell sideways onto the couch and flipped over to face the wall. The Doctor settled himself back into the chair. He seemed to be more comfortable in a sitting position.

"Now, now. Tell the Doctor what's wrong," he said, clearly enjoying his pun. "I'll fix it straightaway."

"Shut up," Sherlock muttered, but he had a trace of a grin on his face as he rolled over to face the Doctor.

"Who is this John fellow? Is this his chair because you bought it from him, or is it his chair in the 'I live here and prefer this chair over the other' kind of thing?"

Sherlock waved his hand at the Doctor. "You know which one."

"Yes, yes, I think I do." he said. "Is there a problem with John? If it's romantic, I'm afraid I can't help you there, not too good at it myself-" Sherlock stood up suddenly, knocking some papers and a pencil off the table. Once up, he didn't seem to know what to do with himself.

"I - John - I don't know! He's gone! He left! I can't find him, I looked everywhere, I went through all his things, no clues, none at all. Nothing to suggest why he left. It's driving me mad!" Sherlock burst out, then became embarrassed. He quickly sat down and regained his composure. The Doctor stood up and cautiously walked over to Sherlock, as though he were a small animal he didn't want to frighten. Sherlock looked up at him and shuddered. The Doctor had worn the look he was wearing now many times before, when Sherlock was a child. He used it when Sherlock was upset, when he dropped his ice cream or scraped his knee.

It was compassion. When Sherlock was younger, he used it in less serious situations, but this time, the stakes were much higher - Sherlock's sanity, and the most important person in his life.

"What's driving you mad - the fact that you can't solve it, or the fact that he's gone?" the Doctor inquired. Sherlock just shook his head.

"Help me find him," he said, getting as close to tears as he ever would. "Just get him back." The Doctor nodded solemnly, putting a reassuring hand on his shoulder.

"I swear to you that I will find him. No matter what circumstances, however dangerous, I will bring him back to you."


	2. Memories

Sherlock remembered vividly - though all his memories were vivid - the first time the Doctor had visited. Sherlock was four, and being forced to play in the back garden with Mycroft. They were sitting at opposite ends, as far away from each other as possible. Sherlock was trying to count all the blades of grass near him. Mycroft was sitting and staring at the sky, thinking about who knows what. They both looked up in surprise when a strange, grating noise began. Neither of them could locate its origin. They looked at each other in a single moment of united confusion.

It ended when, against all logic, a police box faded in and out of view, until finally materializing completely right smack in between the brothers. A man wearing a bow tie stepped out. "Oh, hello! I've found the right place then. And apparently the right time, excellent!" Mycroft stayed sitting down, but Sherlock stood up and ran towards the funny man with the big blue box. He stroked the side, and stared up at the man in wonder.

"Who _are_ you?" he asked, perplexed.

"I'm the Doctor. You're Sherlock, aren't you? Rather a funny name. Oh, and Mycroft! What a pleasure." Mycroft didn't move. He shrunk further back into his corner of the yard.

"How do you know my name?" he asked timidly.

"I know everything about you! I'm your great-great-great-great-great- oh, you get the point - grandfather," the Doctor explained. Mycroft obviously doubted this, and ran in fright to the house. Sherlock looked at him smugly. He knew that Mycroft would be missing out on the greatest adventure of all.

Sherlock doubted that he was, however distantly, related to this man, but he humored the stranger and said, "Prove it."

"Hm, that's a tough one. You get right down to business, don't you?" he asked, ruffling Sherlock's hair. Sherlock flattened it out again, annoyed, and crossed his arms.

"Prove it," he repeated, more insistently this time. The Doctor muddled around for a minute, turning around and turning back, then finally appearing to figure out how best to go about proving their relationship.

He put his hands on Sherlock's shoulders and steered him towards the police box. "In we go," he said, and they entered the most fantastic place, something that boggled the young boy's mind and left him dumbfounded for years.

The box, which appeared ordinary, if slightly blue, on the outside, was enormous on the inside. Sherlock stopped and stared, spellbound by the beauty and impossibility of it. The Doctor leaned against a railing, looking at him expectantly. Sherlock turned his gaze onto this wondrous man and said, "It's smaller on the outside."

The Doctor appeared to be stalled for a second by this comment, then resumed his usual manner. "Quite right - I mean, most people switch it around, you know, "It's bigger on the inside!" but I like your thinking, quite out of the box - or rather, in it!" He reached out to pat the young Sherlock on his head again, but he managed to duck out of the way.

"Don't _do_ that," he complained, crossing his arms again.

"Oh, all right. Anyway, you want proof? You're getting proof. If you would step this way," the Doctor said, gesturing to a screen. "This is going to scan your entire body to find any traces of me in it, okay? Won't hurt a bit." Sherlock stood completely still.

"You know, I know lots of science, you don't have to make it easy for me," he said out of the corner of his mouth.

"I don't doubt that, no, not at all - it's me that doesn't get it," the Doctor assured him. Sherlock resisted the urge to roll his eyes - grown-ups never understood that he knew much more, so much more than they did. At that moment, there was a ping, and the Doctor pulled the screen down to Sherlock's height so he could take a look. "There you are - proof. You are my direct descendant."

"How do I know you're not lying? What if this is a fake?" asked Sherlock. As much as he wanted to believe it was real. It was just too good to be true, that he was related to some supernatural being.

"I have a police box that appeared out of nowhere that's bigger on the inside and you're asking me whether I faked all this? Your answer is a resounding no," the Doctor replied. Sherlock had a feeling that this was the truth, and from that point on, everything the Doctor said would be taken as absolute, undeniable truth. Which was not always a smart thing to do.


	3. The Investigation

**Sorry that I haven't updated this in FOREVER. There's no excuses, really, I just hope you enjoy it. This is obviously pre-Reichenbach.**

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><p>Back in the present, the Doctor was in John's room. Sherlock was standing in the doorway with a horrified look. The Doctor's inspection was nothing like Sherlock's had been. Sherlock had worn gloves, touched everything with the utmost reverence and caution. He had taken small sentimental things - John's phone, which John had mysteriously not taken with him; one of his jumpers, which still smelled like him; his shampoo, which Sherlock had used ever since, even though his hair type was completely different. Sherlock had frantically come up with an excuse for the missing items by the time the Doctor had entered John's room, but it looked like he wouldn't be needing it.<p>

To put it nicely, the Doctor had a unique way of looking for clues - tearing the room apart. First, he grabbed hold of the covers on the bed and yanked them back. "Well, looks like he isn't here," the Doctor said matter-of-factly. "It's funny, that's usually the place people forget to look, and also the place people turn up in." Then he lay flat on his stomach and peered under the bed. "Not here, either!" he called. Sherlock rolled his eyes. This man was ten times older than Sherlock could ever hope to be, and yet never failed to act like a five year old. It would almost be endearing, if the situation weren't so serious. The Doctor started viciously pulling open drawers and tossing out their contents. He was completely wrecking the only bit of John Sherlock had left.

"STOP!" he screamed, his voice nearly breaking. The Doctor stood up quickly, half raising his hands in a gesture of surrender. In three steps, Sherlock had crossed the room and gripped the Doctor by his shoulders. In a low, menacing voice, he assured him, "If you aren't going to be serious about this, you can jump back into that obscenely blue box of yours and fly across the universe, far - away - from - me." He shook the Doctor with each word. Sherlock turned then, and slowly fixed the bed and placed John's possessions back in the drawers.

"I'm sorry, I really am," said the Doctor. "But it's very unusual not to have any sign _at all_ of a person's disappearance. Usually there's something out of order, something strange. I mean," he continued, pacing quickly around the edge of the room, "if I didn't know you better...I would have thought you put this together by yourself. It's almost like a very thorough stage, assembled by someone who knew John very well. Look!" he said, dashing to where John's disused cane was resting against the wall. "This cane is a work of art," the Doctor proclaimed dramatically. "It's in a corner, out of the way, obviously because he doesn't use it, but it's still in sight. That shows he's either worried he'll need it again or it's sentiment. Someone who was putting a room together would have forgotten the cane, or left it lying around somewhere in a closet." The Doctor, still crouching by the cane in the corner, glanced up at Sherlock, who was peering over his shoulder. Sherlock straightened up, then sat carefully down on the bed.

"Don't bother me," he murmured. "I'm going to my mind palace." Without a word, the Doctor settled into a chair. He fondly watched the process he'd seen many times before, discreetly filming it so he could play it back for Amy and Rory later. Sherlock waved his hands around, up and down, side to side. Finally, his eyes snapped open, his face full of wonder, fear, and disgust. "A creature," he whispered. "One with a skeletal figure, with a face like skin stretched over a skull. And wearing a...suit," he added, mystified.

"That's impossible!" the Doctor exclaimed, ecstatically. He reached over and hugged Sherlock, who gingerly returned the hug.

"What is?" he asked. He was used to being told he was impossible, unreal, out of the ordinary. But that was from people like Lestrade or John. The Doctor did not hand out praise so easily, though. Sherlock had always clamored for the elusive praise of the Doctor. It shouldn't have mattered to him, but it did. With John gone now, Sherlock had been finding admiration less and less often.

"That you _remembered_!" the Doctor cried. "What you just described is an alien race, one that can subtly alter events by suggesting you do them and erasing their presence from your memory, but allowing the suggestions to live on. What you just did defied their entire existence. You must have held on to its image as well as the tasks it asked you to perform. Based on what you and I just said, a Silence came in here, took John, sent him away somewhere, and waited until you came home to ask you to put his room back together so that looking back at it later, you wouldn't be able to tell that anything had been touched, or that there was a struggle of some kid," he said all this very fast, and very excitedly. "Now _that's_ something to go on. It also explains why my TARDIS decided to drag me here instead of Barcelona. The planet, not the city."

Sherlock nodded, taking everything in while his mind whirred, coming up with plans and schemes and disguises. "Why are we wasting our time?" he asked, staring at the Doctor. "Let's go."


End file.
